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I think its a frame and caliper combination thing. Not every frame is going to be exactly the same. Different specifications exist on where brakes should be placed although they should all be very similar. The hope caliper on my road bike fouled on the rotor and needed slightly spacing. Others use the same calipers on other bikes with no spacers. 2-3mm is not going to be a machining QC issue, that's several tens of times more than an acceptable machining tolerance
Yes, the faces of the mounting points on the old calipers must have had too much material machined off or something along those lines.
Just strange that a QC issue like that could happen.